marcguery/malaria-barcodes-genomes-gambia
Domain:
healthcareRecord type:
dataset
Creator:
mar
Host:
# Scripts, data and figures of Guery *et al.* 2024
This repository contains the pipeline, data and figures included in:
Guery, M.-A., Ceesay, S., Drammeh, S., Jaiteh, F. K., d’Alessandro, U., Bousema, T., Conway, D. J., & Claessens, A. (2024). Household clustering and seasonal genetic variation of Plasmodium falciparum at the community-level in The Gambia. *eLife*, *13*. doi.org.
# Pipeline
The details of this pipeline are described in the methods section of the corresponding article.
The script `barcode-genome_pipeline.R` is the main script controlling each step of the pipeline. Beware that some steps require the output of previous ones.
The script `make-tables.R` uses the output of the pipeline to produce the tables attached with the article.
## Environment
The pipeline was run with R version 4.3.3 on Ubuntu 22.
```R
─ Session info ────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.3.3 (2024-02-29)
os Ubuntu 22.04.5 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate C.UTF-8
ctype C.UTF-8
tz Europe/Paris
date 2025-01-21
rstudio 2024.12.0+467 Kousa Dogwood (desktop)
pandoc 2.9.2.1 @ /usr/bin/pandoc
─ Packages ────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
ape * 5.7-1 2023-03-13 [1] CRAN (R 4.3.2)
binom * 1.1-1.1 2022-05-02 [1] CRAN (R 4.3.3)
BiocGenerics * 0.48.1 2023-11-01 [1] Bioconductor
cli 3.6.3 2024-06-21 [1] CRAN (R 4.3.3)
colorspace 2.1-1 2024-07-26 [1] CRAN (R 4.3.3)
cowplot * 1.1.3 2024-01-22 [1] CRAN (R 4.3.2)
digest 0.6.36 2024-06-23 [1] CRAN (R 4.3.3)
dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.3.2)
fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.2)
farver 2.1.2 2024-05-13 [1] CRAN (R 4.3.3)
generics 0 …